How To Get The Effect Of A Snp On A Transcript Via Eutils

Question

[Andrea_Bio]

Esteemed bioinformaticians

I was wondering if anyone on here has a local copy of dbSNP and could answer me some questions before i undergo what i have been told is a painful process of installing a local copy.

I have looked at all of these Entrez SNP reports and none of them give me the information I want. I want to get the information about how the SNP affects the transcript as show in the GeneView section of the webpage. Some reports do show you some of this information - this is a snippet of the flat file report from rsrs2034920

LOC | CT45A5 | locusid=441521 | fxn-class=coding-synonymous | allele=C | frame=3 | residue=N | aaposition=97<BR> LOC | CT45A5 | locusid=441521 | fxn-class=reference | allele=T | frame=3 | residue=N | aaposition=97<BR> LOC | CT45A5 | locusid=441521 | fxn-class=coding-synonymous | allele=C | frame=3 | residue=N | aaposition=97<BR> LOC | CT45A5 | locusid=441521 | fxn-class=reference | allele=T | frame=3 | residue=N | aaposition=97<BR> LOC | CT45A5 | locusid=441521 | fxn-class=coding-synonymous | allele=C | frame=3 | residue=N | aaposition=97<BR> LOC | CT45A5 | locusid=441521 | fxn-class=reference | allele=T | frame=3 | residue=N | aaposition=97<BR>

You can't link the consequence info in this report to any particular transcript. There is no transcript information other than this in the whole report.

So i was wondering,

1) Am i missing something obvious and i get the information i want from these reports 2) Presumbably a local copy of dbSNP will contain all of the information used on the webpages so i can get the information from here as a last resort

Please note, I don't want to use any other SNP effect prediction tools like ensembl or snp nexus to get snp consequence - it has to be dbSNP.

my humble thanks

Answer 1

[Pierre Lindenbaum]

The information you want is available in the XML report.

<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001007551" mrnaVer="3" protAcc="NP_001007552" protVer="1" fxnClass="coding-synonymous" readingFrame="3" allele="C" residue="N" aaPosition="96"/>
<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001007551" mrnaVer="3" protAcc="NP_001007552" protVer="1" fxnClass="reference" readingFrame="3" allele="T" residue="N" aaPosition="96"/>
<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001007551" mrnaVer="2" protAcc="NP_001007552" protVer="1" fxnClass="coding-synonymous" readingFrame="3" allele="C" residue="N" aaPosition="96"/>
<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001007551" mrnaVer="2" protAcc="NP_001007552" protVer="1" fxnClass="reference" readingFrame="3" allele="T" residue="N" aaPosition="96"/>
<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001172288" mrnaVer="1" protAcc="NP_001165759" protVer="1" fxnClass="coding-synonymous" readingFrame="3" allele="C" residue="N" aaPosition="96"/>
<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001172288" mrnaVer="1" protAcc="NP_001165759" protVer="1" fxnClass="reference" readingFrame="3" allele="T" residue="N" aaPosition="96"/>

[Andrea_Bio]

what is the rettype of that report as none of the reports in the list i looked at look like that. Is it native? I think that's the default. I know you're a java programmer but I don't know if you use perl. What would you recommend for parsing xml in perl? thanks a lot

[Andrea_Bio]

that report wasn't in the list of reports at ncbi! However the rettype=native report doesn't give the snp allele information. There is some info for the individual submitters but i don't want to use that. I want to use the allele mapped to a specific assembly and if your snp is intronic or the like (e.g. only has one consequence for all the different alleles) you can't get the snp allele from this report

Answer 2

[Giovanni M Dall'Olio]

I am not sure whether I understood your question correctly, but did you try with Biomart?

Go to biomart, select Ensembl, then DATABASE>Ensembl Variation and DATASET>dbSNP, then in the Attributes section you can get information like 'phenotype description' under 'Sequence variation' and 'Transcript ID' under 'Gene Associated Information'.

[Andrea_Bio]

i've never used biomart - will have a look

[Andrea_Bio]

giovanni i was wondering if you were still looking at this question as i have some things i would like to ask

[Giovanni M Dall'Olio]

don't worry, ask them and open a new question if you feel it is necessary... I am not a biomart expert but I will try to answer.